Pfam entry reviews — proposed GO where InterPro can't, with member verification
Index of the curated per-Pfam entry reviews under
interpro/pfam/<PFAM>/<PFAM>-review.yaml(schema:src/ai_gene_review/schema/pfam_entry_review.yaml). Each proposal is grounded in characterized SwissProt members and tested against counter-examples; a family whose own members are functionally heterogeneous is recorded as REJECTED. Validate withjust validate-pfam-reviews. See parent project.
Proposed (5 families)
| Pfam | family | review | relation | proposed GO | aspect | conf. | example |
|---|---|---|---|---|---|---|---|
| PF02431 | Chalcone | PF02431-review.yaml |
enables | GO:0045430 chalcone isomerase activity | MF | HIGH | UniProt:P41088 |
| PF07228 | SpoIIE | PF07228-review.yaml |
involved in | GO:0030435 sporulation resulting in formation of a cellular spore | BP | HIGH | UniProt:P37475 |
| PF09043 | Lys-AminoMut_A | PF09043-review.yaml |
enables | GO:0047826 D-lysine 5,6-aminomutase activity | MF | MEDIUM | UniProt:E3PRJ5 |
| PF16552 | OAM_alpha | PF16552-review.yaml |
enables | GO:0047831 D-ornithine 4,5-aminomutase activity | MF | MEDIUM | UniProt:E3PY96 |
| PF27512 | LeuD | PF27512-review.yaml |
enables | GO:0003861 3-isopropylmalate dehydratase activity | MF | HIGH | UniProt:P30126 |
| PF27512 | LeuD | PF27512-review.yaml |
involved in | GO:0009098 L-leucine biosynthetic process | BP | HIGH | UniProt:P30126 |
Rejected on member verification (4 families)
These families are named for a function but their reviewed members are functionally heterogeneous (counter-examples in the same family), so the term would over-annotate even at the Pfam level.
| Pfam | family | review | term that does NOT hold | why (same-family counter-example) |
|---|---|---|---|---|
| PF13360 | PQQ_2 | PF13360-review.yaml |
GO:0043165 Gram-negative-bacterium-type cell outer membrane assembly | RQKA_DEIRA (DNA-damage-responsive Ser/Thr protein kinase RqkA) (2.7.11.1) |
| PF13561 | adh_short_C2 | PF13561-review.yaml |
GO:0016631 enoyl-[acyl-carrier-protein] reductase [NAD(P)H] activity | FABG_ECOLI (3-oxoacyl-[acyl-carrier-protein] reductase FabG) (1.1.1.100) |
| PF14681 | UPRTase | PF14681-review.yaml |
GO:0004845 uracil phosphoribosyltransferase activity | UCKL1_HUMAN (uridine-cytidine kinase-like 1) (2.7.1.48) |
| PF16363 | GDP_Man_Dehyd | PF16363-review.yaml |
GO:0008446 GDP-mannose 4,6-dehydratase activity | GALE_HUMAN (UDP-glucose 4-epimerase) (5.1.3.2) |